*** empty log message ***

Cantera/cxx/include/Cantera.h

@@ -21,7 +21,7 @@ using namespace std;
 // The Cantera logger class
 #include "kernel/logger.h"
 
-using namespace Cantera;
+//using namespace Cantera;
 
 #endif
 

Cantera/src/CVodesIntegrator.cpp

@@ -11,19 +11,8 @@
 #include <iostream>
 using namespace std;
 
+#ifdef SUNDIALS_VERSION_22
 
-// sundials includes
-#ifdef SUNDIALS_VERSION_1
-#include <sundialstypes.h>
-#include <sundialsmath.h>
-#include <cvodes.h>
-#include <cvdense.h>
-#include <cvdiag.h>
-#include <cvband.h>
-#include <cvspgmr.h>
-#include <nvector.h>
-#include <nvector_serial.h>
-#else
 #include <sundials_types.h>
 #include <sundials_math.h>
 #include <cvodes.h>
@@ -31,8 +20,27 @@ using namespace std;
 #include <cvodes_diag.h>
 #include <cvodes_spgmr.h>
 #include <cvodes_band.h>
-//#include <nvector.h>
 #include <nvector_serial.h>
+
+#else
+
+#ifdef SUNDIALS_VERSION_23
+#include <sundials/sundials_types.h>
+#include <sundials/sundials_math.h>
+#include <sundials/sundials_nvector.h>
+#include <nvector/nvector_serial.h>
+#include <cvodes/cvodes.h>
+#include <cvodes/cvodes_dense.h>
+#include <cvodes/cvodes_diag.h>
+#include <cvodes/cvodes_spgmr.h>
+#include <cvodes/cvodes_band.h>
+
+#else
+
+unsupported sundials version!
+
+#endif
+
 #endif
 
 inline static N_Vector nv(void* x) {

Cantera/src/CVodesIntegrator.h

@@ -24,13 +24,14 @@
 #include "ct_defs.h"
 
 //#include <nvector.h>
-#include <nvector_serial.h>
+//#include <nvector_serial.h>
 
+#include <sundials/sundials_nvector.h>
 
 namespace Cantera {
 
     class FuncData;
-
+    
     /**
      * Exception thrown when a CVODES error is encountered.
      */

config.h.in

@@ -1,5 +1,5 @@
 //
-//  Run the 'configure' script to generate 'config.h' from this input file.
+//  Run the 'preconfig' script to generate 'config.h' from this input file.
 //
 #ifndef CT_CONFIG_H
 #define CT_CONFIG_H
@@ -7,11 +7,6 @@
 
 //------------------------ Development flags ------------------//
 //
-// These flags turn on or off features that are still in 
-// development and are not yet stable. 
-
-#define DEV_EQUIL  
-
 // Compile in additional debug printing where available.
 // Note, the printing may need to be turned on via a switch.
 // This just compiles in the code.
@@ -47,13 +42,11 @@ typedef  int          ftnlen;       // Fortran hidden string length type
 
 
 #undef HAS_SUNDIALS
+#undef SUNDIALS_VERSION_22
+#undef SUNDIALS_VERSION_23
 
 //-------- LAPACK / BLAS ---------
 
-// Define if you are using LAPACK and BLAS from the Intel Math Kernel
-// Library 
-#undef HAVE_INTEL_MKL
-
 #define LAPACK_FTN_STRING_LEN_AT_END
 #define LAPACK_NAMES_LOWERCASE
 #define LAPACK_FTN_TRAILING_UNDERSCORE

configure.in

@@ -306,13 +306,20 @@ sundials_inc=
 CVODE_LIBS='-lcvode'
 IDA_LIBS=''
 
+if test "x$SUNDIALS_HOME" = "x"; then
+SUNDIALS_LIB_DIR=/usr/local/sundials/lib
+SUNDIALS_INC_DIR=/usr/local/include/sundials
+else
+SUNDIALS_LIB_DIR=$SUNDIALS_HOME/lib
+SUNDIALS_INC_DIR=$SUNDIALS_HOME/include
+fi
+
 if test "$USE_SUNDIALS" = "default"; then
 ldsave=$LDFLAGS
-LDFLAGS='-L'$SUNDIALS_HOME/lib' '$ldsave
+LDFLAGS='-L'$SUNDIALS_LIB_DIR' '$ldsave
 
 AC_CHECK_LIB(sundials_cvodes, CVodeCreate, [use_sundials=1], [use_sundials=0],\
 [-lsundials_cvodes -lsundials_nvecserial -lm])
-less conftest.c
 
 LDFLAGS=$ldsave
 fi
@@ -324,12 +331,20 @@ fi
 if test ${use_sundials} = 1; then
 AC_DEFINE(HAS_SUNDIALS)
 echo "using CVODES from SUNDIALS... Sensitivity analysis enabled."
+
 CVODE_LIBS='-lsundials_cvodes -lsundials_nvecserial' 
 IDA_LIBS='-lsundials_ida -lsundials_nvecserial' 
+
+if test "$SUNDIALS_VERSION" = "2.2"; then
+AC_DEFINE(SUNDIALS_VERSION_22)
 sundials_include='-I'${SUNDIALS_HOME}'/include -I'${SUNDIALS_HOME}'/include/sundials -I'${SUNDIALS_HOME}'/include/cvodes -I'${SUNDIALS_HOME}'/include/ida'
+else
+AC_DEFINE(SUNDIALS_VERSION_23)
+sundials_include='-I'${SUNDIALS_INC_DIR}
 echo "sundials include directory: " ${sundials_include}
-echo "sundials library directory: " $SUNDIALS_HOME/lib
-python tools/src/sundials_version.py $SUNDIALS_HOME
+echo "sundials library directory: " $SUNDIALS_LIB_DIR
+# python tools/src/sundials_version.py $SUNDIALS_HOME
+fi
 fi
 
 if test ${use_sundials} = 0; then

ext/f2c_libs/arith.h

@@ -1,3 +1,3 @@
 #define IEEE_8087
 #define Arith_Kind_ASL 1
-#define Double_Align
+#define NANCHECK

preconfig

@@ -234,31 +234,41 @@ ENABLE_TPX='y'
 #         CVODE / CVODES
 #-----------------------------------------------------------------
 # 
-# Cantera uses the CVODE ODE integrator to time-integrate reactor
-# network ODE's and for various other purposes. An older version of
-# CVODE comes with Cantera, but it is possible to use the latest
-# version as well, which now supports sensitivity analysis (CVODES).
-# CVODES is a part of the 'sundials' package from Lawrence Livermore
-# National Laboratory. Sundials is not distributed with Cantera, but
-# it is free software that may be downloaded and installed
-# separately. If you have sundials, set SUNDIALS_HOME to the directory
-# where it is installed, or else put the sundials libraries on the
-# library path.  If you leave USE_SUNDIALS = 'default', then it will
-# be used if you have it, and if not the older CVODE will be used. Or
-# set USE_SUNDIALS to 'y' or 'n' to force using it or not.  Note that
-# sensitivity analysis with Cantera requires use of sundials.
+# Cantera uses the CVODE or CVODES ODE integrator to time-integrate
+# reactor network ODE's and for various other purposes. An older
+# version of CVODE comes with Cantera, but it is possible to use the
+# latest version as well, which now supports sensitivity analysis
+# (CVODES).  CVODES is a part of the 'sundials' package from Lawrence
+# Livermore National Laboratory. Sundials is not distributed with
+# Cantera, but it is free software that may be downloaded and
+# installed separately. If you leave USE_SUNDIALS = 'default', then it
+# will be used if you have it, and if not the older CVODE will be
+# used. Or set USE_SUNDIALS to 'y' or 'n' to force using it or not.
+# Note that sensitivity analysis with Cantera requires use of
+# sundials.
 #
 # See: http://www.llnl.gov/CASC/sundials
 #
 USE_SUNDIALS=${USE_SUNDIALS:='default'}
-SUNDIALS_HOME=${SUNDIALS_HOME:=$HOME/sundials}
-#SUNDIALS_VERSION=${SUNDIALS_VERSION:='2.2.0'}
+
+# This is where you installed sundials if you used the --prefix option
+# when you configured sundials. If you didn't use the prefix option,
+# then comment this line out.
+SUNDIALS_HOME=${SUNDIALS_HOME:=$HOME/sundials23}
+
+# It is recommended that you install the newest release of sundials 
+# (currently 2.3.0) before building Cantera. But if you want to use an 
+# older version, set SUNDIALS_VERSION to the version you have.
+# Acceptable values are '2.2' and '2.3' only; anything else will cause
+# Cantera to not use sundials.
+SUNDIALS_VERSION=${SUNDIALS_VERSION:='2.3'}
+
 
 #----------------------------------------------------------------- 
 #         BLAS and LAPACK
 #-----------------------------------------------------------------
 #
-# Cantera comes with Fortran versions of those parts of BLAS and
+# Cantera comes with Fortran (or c) versions of those parts of BLAS and
 # LAPACK it requires. But performance may be better if you use a
 # version of these libraries optimized for your machine hardware. If
 # you want to use your own libraries, set BLAS_LAPACK_LIBS to the
@@ -267,7 +277,7 @@ SUNDIALS_HOME=${SUNDIALS_HOME:=$HOME/sundials}
 # libraries are located. Otherwise, leave these lines commented out.
 #
 #BLAS_LAPACK_LIBS='-llapack -lblas'
-#'-llapack -lf77blas -lcblas -latlas'
+#BLAS_LAPACK_LIBS'-llapack -lf77blas -lcblas -latlas'
 #BLAS_LAPACK_DIR='/usr/lib'
 #
 # Note that on Mac OSX, BLAS and LAPACK from the built-in 'Accelerate'
@@ -308,13 +318,12 @@ CXXFLAGS=${CXXFLAGS:="-O3 -Wall"}
 
 # the C++ flags required for linking. Uncomment if additional flags
 # need to be passed to the linker.
-#LCXX_FLAGS="-framework Accelerate"   
 
 # Ending libraries to tack onto the linking of all C++ programs
 LCXX_END_LIBS=${LCXX_END_LIBS:="-lm"}
 
-# the compiler flag to use to compile code that will be inserted into shared 
-# libraries. 
+# the compiler flag to use to compile code that will be inserted into
+# shared libraries.
 PIC=${PIC:=-fPIC}
 
 # the compiler option to create a shared library from object files
@@ -372,9 +381,13 @@ RANLIB=${RANLIB:="ranlib"}
 # doesn't work, try GNU make.
 MAKE=${MAKE:=make}
 
-# The directory location of the graphviz program, dot.
-# dot is used for creating of the documentation.
-# if "dot" is in your path, you can leave this unspecified.
+# The directory location of the graphviz program, dot.  dot is used
+# for creating the documentation, and for making reaction path
+# diagrams.  if "dot" is in your path, you can leave this unspecified.
+#
+# NOTE: MATLAB comes with a stripped-down version of 'dot'. If 'dot'
+# is on your path, make sure it is not the MATLAB version!
+#
 GRAPHVIZDIR=${GRAPHVIZDIR:=" "}
 
 # file extensions